biochem chp 2 water

physical properties of water

melting point - 0 C

boiling point - 100 C

heat of vaporization - 2260 J/g

bc of noncovalent interactions

geometry of water / dipoles

e- geometry - tetrahedral (ish)

molecular geometry - bent

Noncovalent interactions

easy to break/ dynamic

• always forming and breaking

salt bridges, H bonds, van der waals

Hydrogen bonds

between Hydrogen bonded to electronegative atom (O, N, S) and lone pair on an electronegative atom

longer than a covalent bond but much weaker

polar molecules bond well, charges do not

water structure in ice

goal: maximize H bonds

ice less dense than liq H20

• will float to top so suff can live underneath

only prt that doesn’t maximize is top bc no other water so will be exposed and less stable

hydrogen bond functions

substrate recognition, enzyme binding

nucleic acid pairing

if lone pair involved in resonance cant accept H bond

most stable h bond geometry (energetically)

linear

(bent not as stable)

ionic bond

charge charge interaction

positive and negative charge => favorable

forms salt bridge

stabilizes different biological reactions

coulombic interactions

like charges

unfavorable

F

Q₁Q₂/Er²

Q = absolute value of charge

r = distance between charges

E = dielectric constant

Dielectric constant

ability of environment to reduce strength of electrostatic

E_H2O = 80

high dielectric charge makes good for screening / can mitigate charges

universal solvent, will always have screening/shielding effect

Van der Waals/London Dispersion Forces

uncharged and uncharged

nonpolar/nonpolar

dipole-dipole interactions

induced dipole

highly dynamic

van der waals interactions components

attractive force (LDF) depends on polarizability

repulsive force (steric repulsion) depends on size of atoms

van der waal radii

larger VDW_r —> weaker interaction

can plot

how do nonpolar molecules dissolve in water

carrier molecules

clathrates

gas channels

carrier molecules

enzymes adapted to carry gasses through the cell

gas channels

small hydrophobic channels for gasses

1 way

clathrates

ordered cage molecules around a guest molecule

guest molecule hydrophobic

higher entropic cost

enthalpy mildly unfavored because not maximizing H bonds

micelles

spherical macro shapes

form under favorable conditions (release of water clusters drives formation)

release of ordered water in biological interactions

when a nonpolar substrate comes into contact with enzyme (also np) ordered water is released as H2O clusters and disordered water is displaced by the interaction

enzyme-substrate interaction stabilized by H bonding, ionic and hydrophobic interactions

strong noncovalent interactions

hydrogen bonds

ionic interactions (attraction/repulsion)

weak noncovalent interactions

hydrophobic interactions

van de waals interactions

pH

=-log[H+]

log scale

pH water = 6.5-8

weak vs strong bases in aqueous solution

strong acid/base completely dissociates into H+ or OH- in aqueous solution

weak acids do not completely dissociate

• proton and conjugate base

• described by dissociation constant

acid dissociation constant (k_a)

k_eq of HA ←→ A- + H+

-logk_a=pk_a

k_a decrease, pk_a increase, pH increase

henderson hasselbach equation

calculate concentrations of the acidic and basic components of the mixture id the pH and pK_a are known

pK_a=pH-log[A-]/[HA]

weak vs strong titration curves

strong has sharp incr/decr (almost vertical)

weak has more gradual less steep incline

relationship between titration curve and pK_a

pH=pK_a at midpoint

buffers

aqueous solutions that can resist change in pH in if small amounts of acid or base are added

“buffering region” the change is very small as a function of added acid or base

pH in biology

enzymes catalysts have optimal pH (extremes can cause problems with metabolism)

low pH —> acidosis

• caused by diabetes, fasting, starvation, etc

• treated by treating underlying cause and/or IV bicarbonate